I need to check out my table feature/rep-seq in terms of contamination. I have more unassigned taxa for functional genes. I have managed to relieve unassigned taxa somewhat using maxaccept parameter in classifiers (Blast+ and Vsearch), but they are still high.
To do this, I installed the ggplot, phyloseq and decontam packages in Rstudio and I checked their versions. I looked at the documentation to get idea how to work with this package, but I did not understand how to use and start this package in order to remove probable decontamination. I have no more experience to work with R (specially this package) that is why I asked the basic question.
Simply I need a workflow with slightly details.
For example, I have no idea about this command’s arguments:
ps <- readRDS(system.file(“extdata”, “MUClite.rds”, package=“decontam”))
What is extdada? What is MUClite.rds? What is RDS?
I would appreciate to help me out.